The Royal Bank of Scotland Group said duplicate mortgage payments have not been taken during Natwest's IT meltdown - but "a small number" of customers with personal loans had been charged twice.
The company moved to clarify the position after reports that some duplicate mortgage payments were mistakenly taken. The RBS issued the latest in a series of apologies to customers and urged them to get in touch so it can put the problems right.
The group said it believes a "small number" of customers have been affected and promised that no one will be left permanently out of pocket.
A spokeswoman said: "We've had questions today about duplicate transactions affecting some customers and we'd like to clarify. A small number of personal loan payments from customers have been debited twice today. We apologise for this and are working hard to put all affected accounts back in order.
"No NatWest or RBS mortgage customer has had their monthly mortgage payment duplicated. A small number of One accounts have debit card transactions showing twice in their account, however these have only been debited once from the account balance.
"We apologise to any customers experiencing problems today. We said last week that we expected to see a few bumps in the road for customers as we get things fully back on track. Any customers experiencing problems should contact our call centre or visit their local branch and we will put things right."
The group has been working "round the clock" to resolve the problems which began two weeks ago and meant NatWest, Ulster Bank and RBS customers' balances were not updating properly.
RBS Group chief executive Stephen Hester said last week that he will forgo his bonus this year because of the chaos and has promised a "full and detailed investigation". Despite facing some calls to quit, he has said he is determined to "personally lead the process" of regaining customers' trust.
The banking group's initial findings were that the problems were created when maintenance on its systems, which are managed and operated by its team in Edinburgh, created an error which stopped people's accounts updating properly. The problem was made worse because the team could not access a record of the transactions that had been processed up to the point of failure.
A "substantial backlog" was created because the group, which processes 20 million transactions a day, had to try to pinpoint the moment at which processing had stopped, which created more delays.